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Move Java sources from src/main/groovy to src/main/java

There are no Groovy sources left, so there's no need to keep these files in src/main/groovy. We can also save build time by only invoking a single compiler instead of two for these projects.

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Mark classpaths as `@Classpath`

Instead of annotating with `@InputFiles` and `@OrderSensitive`, we now have only `@Classpath`.

This also enables relative path normalization for every classpath property.

+review REVIEW-6241

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Mark all classpath task properties order-sensitive

All classpaths should respect file order.

+review REVIEW-6114

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Mark any un-annotated task properties with `@Internal`

+review REVIEW-5932

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Removed duplicate package-info files

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fix duplicated start scripts in application plugin

- create startscripts marks output folder _AND_ windows/unix scripts as output files. This causes duplicate files when referencing CreateStartScripts#outputs.

- removed @OutputFile annnotation for unix and windows script as they are generated from output directory + application name

- updated integration test to check for duplicate files in default application distributions

+review REVIEW-5484

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Add a Groovy subclass for binary compatibility.

+review REVIEW-5416

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JvmBinarySpec extends BaseBinarySpec

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Moved `org.gradle.api.jvm.ClassDirectoryBinarySpec` to `org.gradle.jvm.ClassDirectoryBinarySpec`

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